Smooth Pebbles

Pacific Salmon take another hit, where it really hurts

Via the invaluable Knight-Ridder Science Journalism Tracker comes woeful news from the L.A. Times: One of the few remaining success stories, the Alaskan salmon fishery, is under threat by a parasite whose expansion seems related to climate change.

I'm trying to finish an unrelated story myself, so will simply post the Tracker's write-up below the photo, which comes from a first-rate photo essay that accompanies Kenneth Weiss's full story at the LA Times. There's also quite a nice video version at the Times' site. (I can't figure out how to embed it here, but it heads the main story.

http://www.latimes.com/media/photo/2008-05/39343633.jpg

More Pacific coast salmon woes. In Alaska’s warming rivers the chinook are getting “ick.”

Up on Alaska’s northernmost, tundra-speckled coast the locals already have complained in recent years that global warming has made it harder to keep meat fresh in their cellars - as permafrost thaws, the ground doesn’t provide a natural freezer in every hole. Now, across more of the state, some salmon are going bad while they’re still swimming. The LA Times’s Kenneth R. Weiss on Sunday had a long feature (and isn’t it nice to find a paper, even the LAT with its buyouts, layoffs, and other thrift, still running such?) on it. An increasing number of salmon pulled from the Yukon and other rivers, gleaming and flopping, are promptly thrown in the “dog pot” as inedible and unmarketable for people. The meat, it says here, turns mealy. Smoked and dried it looked more like “strips of greasy rotten mango” than the intended rich red jerky.

The fish have a form of the parasitic disease ich, pronounced ick (familiar to many aquarium-owning fish hobbyists), reports Weiss. His piece lays out the rise of its incidence, suspicion that the warming water has made the fish more susceptible in the last 20 years, and a scientific and regulatory ruckus that pitted factions within the fishing industry and state fish and game officials over the problem’s urgency. The issue, it appears from this piece, has been a hot one for some time there. Weiss gives it a needed, more national stage and presents it as an example of the changing landscape of wildlife diseases.

Included, in this age of converging media, is a photo gallery online and a well-done video version.

It’s a colorful package with many cited sources. The Tracker would have had plenty more questions for the researchers about the disease’s dynamics and the hypothesized link to warmer water. Such as - do young salmon probably catch it on their way out of the rivers, then worsen when they migrate back from the sea to spawn? Do salmon in rivers farther south, from Canada down into California where rivers presumably have been this warm all along, get ich - or might subpopulations there have developed resistance? (LATE ADDITION: Weiss says he asked. No answer yet and room in the news hole for questions that have no answers is rare). But this yarn is convincing as it stands. Something has changed. Temperature is a prime suspect.

Technorati Tags:
salmon, climate_change, commercial_fishing

Pebbles I stumbled on this week (notables from the web)

A Chopin Nocturne...

from Derek Bownds' MindBlog by noreply@blogger.com (Deric)

Bownds blogs on neuro matters -- and, each week, posts a video of him playing a bit of classical music on his piano. Gotta like it.

FDA To Mine Big Databases For Safety Problems

from Pharmalot

The effort, called Sentinel Initiative,
will be the first time the FDA will have an opportunity to monitor
almost immediately how drugs are affecting the public. To do so, the
agency will mine databases of more than 20 million patients who receive
their drugs through Medicare. The idea, of course, is to catch side
effects that might otherwise go undetected for months or years.

Also covered at the Wall Street Journal Health Blog

A Musical Aptitude Section Of The Genome?

from Scientific Blogging - Neuroscience

Molecular and statistical genetic studies in 15 Finnish families have shown that there is a substantial genetic component in musical aptitude.

Musical aptitude was determined using three tests: a test for auditory structuring ability (Karma Music test), and the Seashore pitch and time discrimination subtests. The study represents the first systematic molecular genetic study that aims in the identification of candidate genes associated with musical aptitude.

File this under "Interesting if true" -- or what scientists call "needs replication."

As General Surgery Ranks Dwindle, Patients May Suffer

from WSJ.com: Health Blog by Sarah Rubenstein

Sexual Dysfunction On Anti-Depressants Higher Than Thought, Longer Lasting

from Furious Seasons by Philip Dawdy

Thanks to CL Psych who flagged this issue the other day and posted one academic paper acknowledging that not only are there weird problems such as genital anesthesia--such a polite term--connected with anti-depressant use in some cases, but that the rate of sexual dysfunction on the happy pills isn't very happy at all. In fact, it's much higher than doctors have commonly assumed and than pharma companies have been willing to admit.

Dawdy -- a fearless chronicler of others' and his own experience with depression and antidepressants -- notes that he himself experienced no sexual side-effects.

The shifting sands of the 'autism epidemic'

from Mind Hacks by vaughan

The Economist has a short but telling article on whether the so-called 'autism epidemic', occasionally touted in the media, may simply be a change in how developmental problems are diagnosed.

It covers a new study that did something really simple - it tracked down 38 people who, years ago, had been diagnosed with a delay in language and re-assessed them using the latest diagnostic interviews.

An Omnidirectional Treadmill Means One Giant Leap for Virtual Reality

My (very short) story on a new omnidirectional treadmill for spatial cognition research is up at the Wired site:

An Omnidirectional Treadmill Means One Giant Leap for Virtual Reality.

...This April, a team based at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany, unveiled the CyberWalk, an omnidirectional treadmill designed to serve as a VR-capable movement platform. Treadmills have been tried in VR before, of course, but early models were unconvincing — either too small to keep goggled wanderers on the platform or too slow, bouncy, or gap-ridden to feel the least bit real. The CyberWalk solves these problems with a stiff, gapless, 20 x 20-foot floor and movement and feedback systems that enable quick, fluid changes of direction.

We know what you're thinking: Halo! But gamers must wait. For now, access goes to spatial-cognition and perception researchers, who will use the CyberWalk to "explore all sorts of things we haven't been able to explore before," says William Thompson, a University of Utah computer scientist. In addition to studying our brains and understanding space and movement, they'll assess potential for military and disaster-response operations and see if the device can be used to treat medical issues such as Parkinson's.

Slate asks: Are MDs shilling for pharma ... on public radio?

In a nifty bit of reporting, veteran health reporters Shannon Brownlee and Jeanne Lenzer revealed in "Stealth Marketers," a story on Slate, that a "Prozac Nation: Revisited," a radio piece on antidepressants and suicide that ran on many public radio stations recently, "featured four prestigious medical experts discussing the controversial link between antidepressants and suicide" who all reportedly have financial ties to the makers of antidepressants -- as does the radio series, known as "The Infinite Mind," that produced the show.

As the story notes, the extent of the financial ties are unknown because those involved won't reveal them. Still, Brownlee and Lenzer argue, the show in question, "Prozac Nation: Revisited," "may stand in a class by itself for concealing bias." (Then follows a troubling paragraph outlining the conflicts of interest involved.)

is that undisclosed financial conflicts of interest among media sources seem to be popping up all over the place these days. Some experts who appear independent are, in fact, serving as stealth marketers for the drug and biotech industries, and reporters either don't know about their sources' conflicts of interests, or they fail to disclose them to the public.

The story goes on to list several examples that point out out badly such influence compromises our ability to trust many news reports.

Conflicts of interest abound even in unexpected places. A recent survey of academic medical centers published in the Journal of the American Medical Association found that 60 percent of academic department chairs have personal ties to industry—serving as consultants, board members, or paid speakers, while two-thirds of the academic departments had institutional ties to industry. Such ties can be extremely lucrative. And according to these articles in the medical literature, researchers who receive funding from drug and medical-device manufacturers are up to 3.5 times as likely to conclude their study drug or medical device works than are researchers without such funding.

Brownlee and Lenzer put some focus on journalists as well. They cite one study of 544 science stories from top outlets (from 4/06 to 4/08) that checked whether the journalists quoted an independent expert and/or made some attempt to report researchers' potential conflicts of interest. "Half the stories failed to meet this requirement."

This doesn't surprise me. This story prompted a very lively exchange on a science writer listserve I participate in. That exchange confirmed that there's wide variation in how consistently researchers (and the institutions they work for) reveal their funding sources and in how often or consistently journalists ASK their sources about their funding resources. Science journalism is a field ever in tension between an excitement over the scientific discoveries in question and the more hard-nosed mission to vet the reported results and examine science as a social, political, and commercial activity. Most science journalists are ever balancing interest and enthusiasm with skepticism and critical thinking. They should do so conscientiously, of course; that's their job.

As Brownlee and Lenzer note, it's impossible to know at this point a) how much money some of the people involved actually got from drug companies and b) of course, how much it influenced them. But it's well-establshed that trust in scientific results -- especially in the much-tainted arena of psychiatric drugs -- depends on a transparency in funding that has been sorely lacking. This sort of thing -- undisclosed funding from pharm interest of a show that purports to EXAMINE the controversy over antidepressants and suicide -- can't help matters.

Technorati Tags:
depression, journalism, Lilly, medicine, pharma, Slate, Brownlee, Jeanne Lenzer

Steroids for the Brain? Nature Survey Finds Many Neuro-Pill-Popping Scientists

We've seen our brain on drugs. Here's the dope on brainy people on drugs.

Survey results of 1400 scientists (or Nature readers, anyway) on use of neuroenhancers
Figure from Nature, "Poll results: look who's doping"

With baseball's steroid scandals seemingly behind us now -- or at least considered less newsworthy -- the press has recently turned some of its steroidal attention to neuroenhancement among major league academics. The journal Nature has taken the lead here, publishing a commentary in early March by two Cambridge University researchers who "reported," as a nicely turned New York Times story by Benedict Carey noted, "that about a dozen of their colleagues had admitted to regular use of prescription drugs like Adderall, a stimulant, and Provigil, which promotes wakefulness, to improve their academic performance. The former is approved to treat attention deficit disorder, the latter narcolepsy, and both are considered more effective, and more widely available, than the drugs circulating in dorms a generation ago."

Carey's article (and others, too; see below) is well worth reading.* But the news today is that Nature ran an open, online survey at its web site and found that 20 percent of those responding said they had used neuroenhancers such as Ritalin (an amphetamine used clinically for ADHD) and modafinil (a "wakefulness promoting" narcolepsy drug that has seen wide off-lable use not only for ADHD and depression but for increasing concentration, working memory, and other cognitive assets).

An online survey is hardly scientific, as it's likely to attract respondents with a, um, demonstrated interest in the subject. And this one was likely further warped by press attention that brought outside (i.e., possibly non-scientists) to take it.

That said, the 20 percent figure won't surprise anyone who hangs out at scientific conferences, where use of modafinil is talked of fairly casually. Many of those who use modafinil consider it a healthy substitute for coffee: better effects, fewer side effects, no demonstrated long-term harm. It sharpens attention, adds stamina, increases the power to resist distraction, and creates a smoother energy curve that lacks the jittery buzz that lots of coffee will predictably create. And some find it interferes less with sleep.

So is this bad? That question seems to flummox everyone. On its face, seemingly so: It's a drug, and we don't take drugs just to boost performance. This sits fine until you think about coffee. Is modafinil is simply a better coffee?These questions make it clear we're on a slippery slope. We'll be seeing a lot more handwringing and headscratching on this one.

Some of the more intriguing coverage so far:

The original Nature commentary, "Professor's little helper." (Nature subscription required)

An interesting pro-con discussion among academics at the Chronicle of Higher Education website.

An advice column at Wired about the competitive threat that neuroenhancement poses in the office environment. The answer, unfortunately, completely the cognitive enhancement of the drug in question (modafinil), advising the non-drug-doer to better his modafinilly enhanced coworker-competitor by working smarter rather than longer.

An fake April Fools Day press release from (not really) the NIH announcing "three new initiatives to fight the use of brain enhancing drugs by scientists." This fooled a lot of bloggers.

* The Carey article visits the inevitable comparisons with steroids in baseball. Some quoted in the article argue that academics taking drugs is different than athletes taking drugs because competition in academics in secondary -- an assertion that may strike many as questionable, given the intense competition not only for tenure but for glory and riches once tenure is secured. The most prominent scientists do well indeed. Those that don't make the cut, not so. As one anonymous scientist said of his thrice-daily does of Adderall in the the Times article, "“I’m not talking about being able to work longer hours without sleep (although that helps). I’m talking about being able to take on twice the responsibility, work twice as fast, write more effectively, manage better, be more attentive, devise better and more creative strategies.”

He makes a good point that is often missed: These drugs don't just pep you up; they sharpen and focus the brain, creating a double enhancement.

What's Under the Rock: Full Data Shows SSRIs Barely Best Placebo

I've written before, both here in Smooth Pebbles and in print, about how FDA policy and drug company practices have allowed drug makers to publish (and the FDA to base approval on) only the most flattering drug-trial results while keeping less-flattering studies in the drawer. Today a New England Journal of Medicine report shows how things change when you include the results from the drawer: The effectiveness of many SSRIs dives to near placebo-level. This despite that the companies design and conduct most of these trials in a way calculated to produce positive results.

When I wrote on this a couple years ago, UCSF professor and Journal of the American Medical Association editor Drummond Rennie, told me, "If a company does ten trials on a drug and two show it helps but eight show it works no better than Rice Krispies, I'm not exactly getting a scientific view if they publish only the two positive studies.... How can we practice sophisticated medicine if the drug companies are hiding their results? That's not science. That's marketing."

The problem remains. Depressing. I recommend a good run.

Benedict Carey has a good story on it at the Times. And here's the meat of the abstract from the NEJM:

Among 74 FDA-registered studies, 31%, accounting for 3449 study participants, were not published. Whether and how the studies were published were associated with the study outcome. A total of 37 studies viewed by the FDA as having positive results were published; 1 study viewed as positive was not published. Studies viewed by the FDA as having negative or questionable results were, with 3 exceptions, either not published (22 studies) or published in a way that, in our opinion, conveyed a positive outcome (11 studies). According to the published literature, it appeared that 94% of the trials conducted were positive. By contrast, the FDA analysis showed that 51% were positive. Separate meta-analyses of the FDA and journal data sets showed that the increase in effect size ranged from 11 to 69% for individual drugs and was 32% overall.

You paid for this research, now you get to read it

The public will soon start getting quicker access to research results it sponsors. From BioMed Central Blog : NIH Public Access Policy to become mandatory:

NIH Public Access Policy to become mandatory

Many open access advocates will already have heard that NIH's Public Access Policy, until now voluntary, is set to become mandatory following President Bush's approval on Dec 26th 2007 of the latest NIH appropriations bill, which includes the following wording:

"The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law."

This is great news both for researchers and for the general public. Peter Suber's January SPARC Open Access Newsletter contains a detailed analysis of what the change means, and identifies some of the key issues that remain to be resolved.

More at BioMed Central Blog : NIH Public Access Policy to become mandatory

Cod, climate, and Nature's new Climate Change journal

A new journal from the Nature Publishing Group (publishers of Nature, Nature Neuroscience, and other favorites of mine) has just started a journal about climate change, and to my delight they feature a story about climate change and Atlantic cod, an old love of mine from my time on the Gulf of Maine.

Atlantic cod, Gadus callarius Linneaus, by Goode, from the magnificent Bigelow and Schroeder, Fishes of the Gulf of Maine, 1953, the best field guide I've ever read, now online.

Cod aren't doing terribly well, because of overfishing and decimation of inshore spawning stocks, though some pockets still produce nice numbers of this lovely fish. The Nature Climate Change story gives a heads-up to a study about how cod fared in previous climate change cycles. This is a hot topic, as many fishermen and scientists wonder whether warming seas have already contributed to the cod's decline so far or might inhibit its recovery. The new study finds that previous large swings in climate have cut cod populations back by as much as a fifth, knocking it down but not out. But the authors don't seem optimistic on how well they'll fare in this one.

Having read a few of these papers, I gather that the jury is still out on how much climate change will complicate the cod's future.

The Natural Environment Research Center actually writes it up more cleanly than the Nature Climate Change story does:

The new findings, published online today (14 November 2007) in Proceedings of the Royal Society B, show that natural climate change has previously reduced the range of cod to around a fifth of present-day values. Despite this, cod continued to populate both sides of the North Atlantic.

The researchers used a computer model and DNA techniques to estimate where cod could be found in the ice age, when colder temperatures and lower sea-levels caused the extinction of some populations and the isolation of others. ....

Professor Bigg [the lead researcher] said "This research shows that cod populations have been able to survive in periods of extreme climatic change, demonstrating a considerable resilience. However this does not necessarily mean that cod will show the same resilience to the effects of future climatic changes due to global warming."

Yet another story, this one from the Telegraph and titled "Climate change joins fishing as cod threat," notes that cod don't do so well in their northernmost ranges:

[The] study by Prof Bigg and colleagues shows that cod "are good at surviving habitat reduction, except in the northern half of their range. With regard to future climate change, it is clear that the acceptable habitat will retreat poleward significantly as temperatures warm," [Bigg] says.

"It is not unlikely that acceptable conditions for spawning will disappear from much of the North Atlantic to become restricted to the Arctic."

Cod is currently not found there, apart from the Barents Sea, and so there is the question of whether the currently depleted species is able to colonise new areas faster than its old habitat is lost, says Prof Bigg.

Yet another paper, meanwhile, by Mieszkowska, Sim, and Hawkins [pdf download], concluded that climate change might already be adding pressure to North Sea cod. The jury will doubtless be out on this one a while. But it raises more worries both about what climate change may do to cod -- and about the difficulty of predicting how different species will fare as things warm up.

A Tour of Neurosci - Mind Matters' First Year

At Mind Matters, the expert-written blog I manage for Scientific American, I've posted a review of the material and papers we covered in that blog's first year. It was interesting to see how the blog echoed the interests of the larger neuroscientific world. The opener:

Mind Matters - The First Year

We did not, alas, make it to the Prague Museum, which is pictured above. But with the end of both the calendar year and Mind Matters' first year it seems a good time to look a back and see where we have been since launching in January.

There's more -- hormones, memory, W's decision-making style -- at the post at Mind Matters. We'll try to get to Prague next year.

Genes, Environment, Depression, and the Free Will Squabble

This week's post at Mind Matters, the Scientific American blog I edit, looks at an intriguing study of gene-environment interactions in abused children. Charles Glatt, who wrote the review, outlines the rather encouraging results of this study, which suggest -- with all the usual caveats about wider applicability and replication of results -- that some reliable nurturing can often override even a triple-whammy of two "bad" genes and an abusive home.

Some readers objected, however, to Glatt's assertion that the study argues well for the idea of free will. One reader wrote:

I see no impact on any discussion of free will in these findings. Are you saying that people who are abused can choose not to be depressed? I don't think that's what you mean.

I see the point of the complaint -- and I don't think that's what Glatt meant. I believe Glatt's broader point is that to the extent that the idea of free will is incompatible with the idea that genes trump experience, the strong and encouraging role that nurturing played in the study he reviewed argues in favor of free will. That argument is strengthened, if in roundabout fashion, if you recognize that gene-environment effects don't merely flick genes on and off but also create a dynamic in which the changing person (changed, i.e., by genetic response to environment) may change in a way that better enables him or her to behave differently, thus changing the environment. A nurturing presence gives me some resilience, increasing my ability to behave constructively.

It gets a bit slippery. Ideed, it starts to erase the fate v. free-will distinction, just as the looping quality of gene-environment interactions (in which environment affects gene expression, which changes behavior, including the ability to change the environment, which in turn affects gene expression) makes moot the either-or choice between nature and nurture. In the end, each is eternally modified by the other, and thus parent and offspring of the other, not terribly unlike an Escher drawing.